# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 19 00:16:16 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: [(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-ethoxy-spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cccc2[C@@H](CN)O[B-]3(O[C@@H]4[C@@H](CO[P]([O-])([O-])=O)O[C@H]([C@@H]4O3)n5cnc6c(N)ncnc56)c12
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 A52  A52  '[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-ethoxy-spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl phosphate'  ligand  60  37  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A52
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 A52  B     B  B     -1   0.596   1.4865  -1.6602   1.3609
 A52  P     P  P      0   1.220  -5.1394  -1.3560  -1.6413
 A52  N1    N  N      0  -0.476   1.5254   5.7166  -0.9854
 A52  O1    O  O      0  -0.556   2.1158  -2.2816   2.5377
 A52  C2    C  CR16   0   0.041   1.9220   4.5094  -1.3818
 A52  N3    N  N      0  -0.452   1.4239   3.3310  -1.0525
 A52  C4    C  CR56   0   0.485   0.3940   3.4470  -0.2163
 A52  C5    C  CR56   0  -0.011  -0.1358   4.6300   0.2765
 A52  C6    C  CR6    0   0.456   0.4871   5.8174  -0.1481
 A52  N6    N  NH2    0  -0.818   0.0771   7.0264   0.2421
 A52  N7    N  N      0  -0.454  -1.1956   4.3792   1.1097
 A52  C8    C  CR15   0   0.106  -1.2951   3.0822   1.1201
 A52  N9    N  NR5    0  -0.543  -0.3595   2.4573   0.3430
 A52  C1'   C  CH1    0   0.178  -0.2204   1.0396   0.1287
 A52  C10   C  CR15   0   0.050   3.2679  -3.0174   2.2559
 A52  C11   C  CR56   0  -0.031   3.4590  -2.9614   0.7609
 A52  C12   C  CR56   0  -0.211   2.4915  -2.1555   0.1856
 A52  C13   C  CR16   0  -0.329   4.4491  -3.6036   0.0207
 A52  C14   C  CR16   0  -0.264   4.4562  -3.4145  -1.3509
 A52  C15   C  CR16   0  -0.398   3.5098  -2.5963  -1.9678
 A52  C16   C  CR6    0   0.282   2.5352  -1.9601  -1.1972
 A52  O1P   O  OP    -1  -0.906  -5.7587  -0.2016  -0.8603
 A52  C2'   C  CH1    0  -0.026   0.0527   0.2150   1.4035
 A52  O2'   O  OC2    0  -0.567   1.3656  -0.1975   1.5325
 A52  O2P   O  O      0  -0.908  -5.4260  -2.7321  -1.0474
 A52  C3'   C  CH1    0  -0.008  -0.7947  -1.0548   1.1931
 A52  O3'   O  OC2    0  -0.570   0.0909  -2.1214   1.2212
 A52  C33   C  CH2    0  -0.291   4.4938  -2.4768   2.9879
 A52  N34   N  NH2    0  -0.799   4.3440  -2.5727   4.4313
 A52  O35   O  O2     0  -0.466   1.5992  -1.1340  -1.7209
 A52  C36   C  CH2    0  -0.182   1.5920  -0.8891  -3.1158
 A52  C37   C  CH3    0  -0.695   0.5487   0.1627  -3.4169
 A52  O3P   O  OP    -1  -0.900  -5.2880  -1.2588  -3.1544
 A52  C4'   C  CH1    0  -0.011  -1.4863  -0.8353  -0.1631
 A52  O4'   O  O2     0  -0.504  -1.4326   0.5701  -0.3887
 A52  C5'   C  CH2    0  -0.135  -2.9221  -1.2957  -0.1946
 A52  O5'   O  O2     0  -0.656  -3.4542  -1.1501  -1.4737
 A52  HN6   H  HNH2   0   0.402   0.5988   7.8451  -0.0191
 A52  HN6A  H  HNH2   0   0.410  -0.6594   7.1289   0.9178
 A52  H8    H  HCR5   0   0.295  -2.0368   2.5237   1.6715
 A52  H1'   H  HCH1   0   0.260   0.6107   0.9093  -0.5709
 A52  H10   H  HCR5   0   0.195   3.1357  -4.0679   2.5717
 A52  H13   H  HCR6   0   0.227   5.1913  -4.2372   0.4928
 A52  H14   H  HCR6   0   0.242   5.2042  -3.9025  -1.9639
 A52  H15   H  HCR6   0   0.260   3.5548  -2.4748  -3.0421
 A52  H2'   H  HCH1   0   0.225  -0.2723   0.7847   2.2864
 A52  H3'   H  HCH1   0   0.207  -1.5585  -1.1571   1.9791
 A52  H33   H  HCH2   0   0.187   5.3806  -3.0058   2.6076
 A52  H33A  H  HCH2   0   0.217   4.6225  -1.4245   2.7167
 A52  HN34  H  HNH2   0   0.334   4.3453  -3.5497   4.7006
 A52  HN3A  H  HNH2   0   0.343   5.1592  -2.1715   4.8773
 A52  H36   H  HCH2   0   0.213   2.5750  -0.5388  -3.4500
 A52  H36A  H  HCH2   0   0.213   1.3728  -1.8133  -3.6634
 A52  H37   H  HCH3   0   0.237   0.4961   0.3172  -4.4947
 A52  H37A  H  HCH3   0   0.237  -0.4406  -0.1357  -3.0706
 A52  H37B  H  HCH3   0   0.232   0.8039   1.1172  -2.9549
 A52  H4'   H  HCH1   0   0.221  -0.9089  -1.3562  -0.9372
 A52  H5'   H  HCH2   0   0.174  -2.9378  -2.3443   0.1390
 A52  H5'A  H  HCH2   0   0.167  -3.4867  -0.7234   0.5577
 A52  H2    H  HCR6   0   0.250   2.7659   4.4974  -2.0631

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 A52  B    O1    single    1.472  0.020  1.472
 A52  B    C12   single    1.624  0.020  1.624
 A52  B    O2'   single    1.478  0.020  1.478
 A52  B    O3'   single    1.476  0.020  1.476
 A52  P    O1P   deloc     1.525  0.020  1.525
 A52  P    O2P   deloc     1.526  0.020  1.526
 A52  P    O3P   deloc     1.523  0.020  1.523
 A52  P    O5'   single    1.706  0.020  1.706
 A52  N1   C2    aromatic  1.331  0.020  1.331
 A52  N1   C6    aromatic  1.338  0.020  1.338
 A52  O1   C10   single    1.396  0.020  1.396
 A52  C2   N3    aromatic  1.321  0.020  1.321
 A52  N3   C4    aromatic  1.332  0.020  1.332
 A52  C4   C5    aromatic  1.387  0.020  1.387
 A52  C4   N9    aromatic  1.364  0.020  1.364
 A52  C5   C6    aromatic  1.406  0.020  1.406
 A52  C5   N7    aromatic  1.371  0.020  1.371
 A52  C6   N6    single    1.335  0.020  1.335
 A52  N7   C8    aromatic  1.301  0.020  1.301
 A52  C8   N9    aromatic  1.367  0.020  1.367
 A52  N9   C1'   single    1.441  0.020  1.441
 A52  C1'  C2'   single    1.543  0.020  1.543
 A52  C1'  O4'   single    1.399  0.020  1.399
 A52  C10  C11   single    1.508  0.020  1.508
 A52  C10  C33   single    1.527  0.020  1.527
 A52  C11  C12   aromatic  1.384  0.020  1.384
 A52  C11  C13   aromatic  1.393  0.020  1.393
 A52  C12  C16   aromatic  1.397  0.020  1.397
 A52  C13  C14   aromatic  1.385  0.020  1.385
 A52  C14  C15   aromatic  1.395  0.020  1.395
 A52  C15  C16   aromatic  1.396  0.020  1.396
 A52  C16  O35   single    1.354  0.020  1.354
 A52  C2'  O2'   single    1.382  0.020  1.382
 A52  C2'  C3'   single    1.541  0.020  1.541
 A52  C3'  O3'   single    1.387  0.020  1.387
 A52  C3'  C4'   single    1.538  0.020  1.538
 A52  C33  N34   single    1.454  0.020  1.454
 A52  O35  C36   single    1.416  0.020  1.416
 A52  C36  C37   single    1.512  0.020  1.512
 A52  C4'  O4'   single    1.424  0.020  1.424
 A52  C4'  C5'   single    1.508  0.020  1.508
 A52  C5'  O5'   single    1.393  0.020  1.393
 A52  C2   H2    single    0.930  0.020  1.080
 A52  N6   HN6   single    0.860  0.020  1.020
 A52  N6   HN6A  single    0.860  0.020  1.020
 A52  C8   H8    single    0.930  0.020  1.080
 A52  C1'  H1'   single    0.970  0.020  1.090
 A52  C10  H10   single    0.970  0.020  1.090
 A52  C13  H13   single    0.930  0.020  1.080
 A52  C14  H14   single    0.930  0.020  1.080
 A52  C15  H15   single    0.930  0.020  1.080
 A52  C2'  H2'   single    0.970  0.020  1.090
 A52  C3'  H3'   single    0.970  0.020  1.090
 A52  C33  H33   single    0.970  0.020  1.090
 A52  C33  H33A  single    0.970  0.020  1.090
 A52  N34  HN34  single    0.890  0.020  1.040
 A52  N34  HN3A  single    0.890  0.020  1.040
 A52  C36  H36   single    0.970  0.020  1.090
 A52  C36  H36A  single    0.970  0.020  1.090
 A52  C37  H37   single    0.970  0.020  1.090
 A52  C37  H37A  single    0.970  0.020  1.090
 A52  C37  H37B  single    0.970  0.020  1.090
 A52  C4'  H4'   single    0.970  0.020  1.090
 A52  C5'  H5'   single    0.970  0.020  1.090
 A52  C5'  H5'A  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 A52  O3'   B    O2'   104.05  3.000
 A52  O3'   B    C12   114.92  3.000
 A52  O2'   B    C12   115.89  3.000
 A52  O3'   B    O1    110.35  3.000
 A52  O2'   B    O1    111.10  3.000
 A52  C12   B    O1    100.68  3.000
 A52  O5'   P    O3P   100.73  3.000
 A52  O5'   P    O2P   104.84  3.000
 A52  O3P   P    O2P   115.20  3.000
 A52  O5'   P    O1P   105.04  3.000
 A52  O3P   P    O1P   114.88  3.000
 A52  O2P   P    O1P   114.02  3.000
 A52  C6    N1   C2    119.08  3.000
 A52  C10   O1   B     114.46  3.000
 A52  H2    C2   N3    116.10  3.000
 A52  H2    C2   N1    115.40  3.000
 A52  N3    C2   N1    128.50  3.000
 A52  C4    N3   C2    111.74  3.000
 A52  N9    C4   C5    105.20  3.000
 A52  N9    C4   N3    128.43  3.000
 A52  C5    C4   N3    126.37  3.000
 A52  N7    C5   C6    132.85  3.000
 A52  N7    C5   C4    110.80  3.000
 A52  C6    C5   C4    116.34  3.000
 A52  N6    C6   C5    122.71  3.000
 A52  N6    C6   N1    119.31  3.000
 A52  C5    C6   N1    117.98  3.000
 A52  HN6A  N6   HN6   118.17  3.000
 A52  HN6A  N6   C6    120.94  3.000
 A52  HN6   N6   C6    120.15  3.000
 A52  C8    N7   C5    104.26  3.000
 A52  H8    C8   N9    121.59  3.000
 A52  H8    C8   N7    124.91  3.000
 A52  N9    C8   N7    113.50  3.000
 A52  C1'   N9   C8    126.89  3.000
 A52  C1'   N9   C4    126.86  3.000
 A52  C8    N9   C4    106.23  3.000
 A52  H1'   C1'  O4'   112.44  3.000
 A52  H1'   C1'  C2'   109.29  3.000
 A52  O4'   C1'  C2'   106.24  3.000
 A52  H1'   C1'  N9    106.60  3.000
 A52  O4'   C1'  N9    107.55  3.000
 A52  C2'   C1'  N9    114.85  3.000
 A52  H10   C10  C33   107.19  3.000
 A52  H10   C10  C11   109.50  3.000
 A52  C33   C10  C11   111.12  3.000
 A52  H10   C10  O1    110.17  3.000
 A52  C33   C10  O1    112.29  3.000
 A52  C11   C10  O1    106.57  3.000
 A52  C13   C11  C12   122.97  3.000
 A52  C13   C11  C10   126.85  3.000
 A52  C12   C11  C10   110.18  3.000
 A52  C16   C12  C11   118.09  3.000
 A52  C16   C12  B     133.87  3.000
 A52  C11   C12  B     108.01  3.000
 A52  H13   C13  C14   120.51  3.000
 A52  H13   C13  C11   121.64  3.000
 A52  C14   C13  C11   117.85  3.000
 A52  H14   C14  C15   118.85  3.000
 A52  H14   C14  C13   120.17  3.000
 A52  C15   C14  C13   120.98  3.000
 A52  H15   C15  C16   121.73  3.000
 A52  H15   C15  C14   118.47  3.000
 A52  C16   C15  C14   119.80  3.000
 A52  O35   C16  C15   123.18  3.000
 A52  O35   C16  C12   116.52  3.000
 A52  C15   C16  C12   120.30  3.000
 A52  H2'   C2'  C3'   111.96  3.000
 A52  H2'   C2'  O2'   111.12  3.000
 A52  C3'   C2'  O2'   106.81  3.000
 A52  H2'   C2'  C1'   109.52  3.000
 A52  C3'   C2'  C1'   103.31  3.000
 A52  O2'   C2'  C1'   113.88  3.000
 A52  C2'   O2'  B     111.24  3.000
 A52  H3'   C3'  C4'   109.33  3.000
 A52  H3'   C3'  O3'   110.93  3.000
 A52  C4'   C3'  O3'   114.51  3.000
 A52  H3'   C3'  C2'   111.14  3.000
 A52  C4'   C3'  C2'   104.48  3.000
 A52  O3'   C3'  C2'   106.25  3.000
 A52  C3'   O3'  B     111.43  3.000
 A52  H33A  C33  H33   106.37  3.000
 A52  H33A  C33  N34   108.75  3.000
 A52  H33   C33  N34   113.22  3.000
 A52  H33A  C33  C10   108.43  3.000
 A52  H33   C33  C10   108.13  3.000
 A52  N34   C33  C10   111.71  3.000
 A52  HN3A  N34  HN34  105.31  3.000
 A52  HN3A  N34  C33   109.17  3.000
 A52  HN34  N34  C33   109.09  3.000
 A52  C36   O35  C16   119.34  3.000
 A52  H36A  C36  H36   107.24  3.000
 A52  H36A  C36  C37   110.43  3.000
 A52  H36   C36  C37   109.63  3.000
 A52  H36A  C36  O35   110.31  3.000
 A52  H36   C36  O35   110.55  3.000
 A52  C37   C36  O35   108.66  3.000
 A52  H37B  C37  H37A  108.51  3.000
 A52  H37B  C37  H37   107.83  3.000
 A52  H37A  C37  H37   108.00  3.000
 A52  H37B  C37  C36   111.29  3.000
 A52  H37A  C37  C36   111.88  3.000
 A52  H37   C37  C36   109.20  3.000
 A52  H4'   C4'  C5'   109.95  3.000
 A52  H4'   C4'  O4'   109.68  3.000
 A52  C5'   C4'  O4'   109.50  3.000
 A52  H4'   C4'  C3'   108.53  3.000
 A52  C5'   C4'  C3'   113.76  3.000
 A52  O4'   C4'  C3'   105.28  3.000
 A52  C4'   O4'  C1'   107.76  3.000
 A52  H5'A  C5'  H5'   106.31  3.000
 A52  H5'A  C5'  O5'   112.16  3.000
 A52  H5'   C5'  O5'   111.87  3.000
 A52  H5'A  C5'  C4'   108.38  3.000
 A52  H5'   C5'  C4'   107.35  3.000
 A52  O5'   C5'  C4'   110.55  3.000
 A52  C5'   O5'  P     117.06  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 A52  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 A52  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 A52  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 A52  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 A52  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 A52  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 A52  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 A52  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 A52  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 A52  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 A52  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 A52  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 A52  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 A52  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 A52  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 A52  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 A52  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 A52  CONST_18  C15   C16  C12  C11     0.00   0.0  0
 A52  CONST_19  C15   C14  C13  C11     0.00   0.0  0
 A52  CONST_20  C14   C13  C11  C12     0.00   0.0  0
 A52  CONST_21  C14   C15  C16  C12     0.00   0.0  0
 A52  CONST_22  C16   C12  C11  C13     0.00   0.0  0
 A52  CONST_23  C16   C15  C14  C13     0.00   0.0  0
 A52  CONST_24  C1'   N9   C4   N3      0.00   0.0  0
 A52  CONST_25  C1'   N9   C4   C5    180.00   0.0  0
 A52  CONST_26  C1'   N9   C8   N7    180.00   0.0  0
 A52  CONST_27  O35   C16  C12  B       0.00   0.0  0
 A52  CONST_28  N6    C6   N1   C2    180.00   0.0  0
 A52  CONST_29  N6    C6   C5   C4    180.00   0.0  0
 A52  CONST_30  N7    C5   C6   N6      0.00   0.0  0
 A52  CONST_31  O35   C16  C12  C11   180.00   0.0  0
 A52  CONST_32  O35   C16  C15  C14   180.00   0.0  0
 A52  CONST_33  H2    C2   N3   C4    180.00   0.0  0
 A52  CONST_34  H8    C8   N9   C4    180.00   0.0  0
 A52  CONST_35  H13   C13  C11  C10     0.00   0.0  0
 A52  CONST_36  H14   C14  C13  C11   180.00   0.0  0
 A52  CONST_37  H15   C15  C16  C12   180.00   0.0  0
 A52  CONST_38  HN6   N6   C6   N1      0.00   0.0  0
 A52  CONST_39  HN6A  N6   C6   N1    180.00   0.0  0
 A52  Var_01    C11   C12  B    O1      1.83  30.0  2
 A52  Var_02    C12   B    O1   C10     0.20  30.0  3
 A52  Var_03    C4'   C5'  O5'  P    -169.41  30.0  1
 A52  Var_04    C37   C36  O35  C16  -174.39  30.0  3
 A52  Var_05    HN34  N34  C33  C10    67.65  30.0  3
 A52  Var_06    H37   C37  C36  O35  -176.81  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A52  chir_01  C1'  N9   C2'  O4'  negativ
 A52  chir_02  C10  O1   C11  C33  negativ
 A52  chir_03  C2'  O2'  C1'  C3'  negativ
 A52  chir_04  C3'  O3'  C4'  C2'  positiv
 A52  chir_05  C4'  O4'  C5'  C3'  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 A52  plan-1  B     0.020
 A52  plan-1  C10   0.020
 A52  plan-1  C11   0.020
 A52  plan-1  C12   0.020
 A52  plan-1  C13   0.020
 A52  plan-1  C14   0.020
 A52  plan-1  C15   0.020
 A52  plan-1  C16   0.020
 A52  plan-1  O35   0.020
 A52  plan-1  H13   0.020
 A52  plan-1  H14   0.020
 A52  plan-1  H15   0.020
 A52  plan-2  N1    0.020
 A52  plan-2  C2    0.020
 A52  plan-2  N3    0.020
 A52  plan-2  C4    0.020
 A52  plan-2  C5    0.020
 A52  plan-2  C6    0.020
 A52  plan-2  N6    0.020
 A52  plan-2  N7    0.020
 A52  plan-2  C8    0.020
 A52  plan-2  N9    0.020
 A52  plan-2  C1'   0.020
 A52  plan-2  H8    0.020
 A52  plan-2  H2    0.020
 A52  plan-3  C6    0.020
 A52  plan-3  N6    0.020
 A52  plan-3  HN6   0.020
 A52  plan-3  HN6A  0.020

